I would suggest that you copy over your 1.4 game folder to another location and rename if you want, just so you can keep track of which version is which. I put my Copy on a different drive (a partition, actually...D:\).
Then
totally Uninstall your original installed version. Here's a very detailed step-by-step procedure to do that. You'll then be able to re-install your SH4 1.4 from the original DVD.
http://www.subsim.com/radioroom/showthread.php?t=133290
Once that is done, you can run either version as you see fit, Modding each differently as you see fit. The only hiccup is that all saved missions will go into the same "Documents\SH4" folder so to keep things straight, Saved missions/files should be named by you using any system to identify which version of the Game they were saved under... (There is a MultiSH4 Application to set up separate "Documents\SH4" folders for each SH4 version, but I do not use it...Do a search and you'll find it).
Good Luck.
P.S. With VISTA, do not install programs into the "C:\Program Files" folder...Vista makes writing to files in that folder difficult/impossible. It can be done running as Adminstrator, but the simpler way that most folks follow is to create a folder such as C:\MyGames and install there all games and other programs to which you will need to write to files.